diff --git a/404.html b/404.html index 86637b0a..3713b019 100644 --- a/404.html +++ b/404.html @@ -40,7 +40,7 @@ spatialLIBD - 1.17.8 + 1.17.9 diff --git a/CODE_OF_CONDUCT.html b/CODE_OF_CONDUCT.html index 80d17f31..a949c361 100644 --- a/CODE_OF_CONDUCT.html +++ b/CODE_OF_CONDUCT.html @@ -17,7 +17,7 @@ spatialLIBD - 1.17.8 + 1.17.9 diff --git a/CONTRIBUTING.html b/CONTRIBUTING.html index e9b5798e..cb41c35a 100644 --- a/CONTRIBUTING.html +++ b/CONTRIBUTING.html @@ -17,7 +17,7 @@ spatialLIBD - 1.17.8 + 1.17.9 diff --git a/SUPPORT.html b/SUPPORT.html index 0f5ba3c3..4bb812f4 100644 --- a/SUPPORT.html +++ b/SUPPORT.html @@ -17,7 +17,7 @@ spatialLIBD - 1.17.8 + 1.17.9 diff --git a/articles/TenX_data_download.html b/articles/TenX_data_download.html index 690f4b9d..b2d33321 100644 --- a/articles/TenX_data_download.html +++ b/articles/TenX_data_download.html @@ -39,7 +39,7 @@ spatialLIBD - 1.17.8 + 1.17.9 @@ -532,7 +532,7 @@

From Gencode## Show the GTF cache location gtf_cache #> BFC4 -#> "/github/home/.cache/R/BiocFileCache/12386af7f0c3_gencode.v32.annotation.gtf.gz" +#> "/github/home/.cache/R/BiocFileCache/123939beec24_gencode.v32.annotation.gtf.gz" ## Import into R (takes ~1 min) gtf <- rtracklayer::import(gtf_cache) @@ -818,11 +818,11 @@

Wrapper functions= c("lowres", "hires", "detected", "aligned"), load = TRUE, reference_gtf = gtf_cache ) -#> 2024-10-22 13:40:03.20411 SpatialExperiment::read10xVisium: reading basic data from SpaceRanger -#> 2024-10-22 13:40:14.744813 read10xVisiumAnalysis: reading analysis output from SpaceRanger -#> 2024-10-22 13:40:14.850538 add10xVisiumAnalysis: adding analysis output from SpaceRanger -#> 2024-10-22 13:40:15.094287 rtracklayer::import: reading the reference GTF file -#> 2024-10-22 13:40:43.097061 adding gene information to the SPE object +#> 2024-10-22 13:44:18.888244 SpatialExperiment::read10xVisium: reading basic data from SpaceRanger +#> 2024-10-22 13:44:30.623699 read10xVisiumAnalysis: reading analysis output from SpaceRanger +#> 2024-10-22 13:44:30.730062 add10xVisiumAnalysis: adding analysis output from SpaceRanger +#> 2024-10-22 13:44:30.973963 rtracklayer::import: reading the reference GTF file +#> 2024-10-22 13:44:58.838561 adding gene information to the SPE object #> Warning: Gene IDs did not match. This typically happens when you are not using #> the same GTF file as the one that was used by SpaceRanger. For example, one #> file uses GENCODE IDs and the other one ENSEMBL IDs. read10xVisiumWrapper() @@ -830,7 +830,7 @@

Wrapper functions#> Warning: Dropping 29 out of 36601 genes for which we don't have information on #> the reference GTF file. This typically happens when you are not using the same #> GTF file as the one that was used by SpaceRanger. -#> 2024-10-22 13:40:43.356885 adding information used by spatialLIBD +#> 2024-10-22 13:44:59.118664 adding information used by spatialLIBD 
 ## Run our shiny app
 if (interactive()) {
@@ -1114,9 +1114,9 @@ 
Reproducibilitylibrary("knitr")
 knit("TenX_data_download.Rmd", tangle = TRUE)

Date the vignette was generated.

-
#> [1] "2024-10-22 13:40:44 UTC"
+
#> [1] "2024-10-22 13:45:00 UTC"

Wallclock time spent generating the vignette.

-
#> Time difference of 1.684 mins
+
#> Time difference of 1.688 mins

R session information.

#> ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
 #>  setting  value
@@ -1281,7 +1281,7 @@ 
Reproducibility#>  SparseArray            1.4.8     2024-05-24 [1] Bioconductor 3.19 (R 4.4.1)
 #>  sparseMatrixStats      1.16.0    2024-04-30 [1] Bioconductor 3.19 (R 4.4.1)
 #>  SpatialExperiment    * 1.14.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.1)
-#>  spatialLIBD          * 1.17.8    2024-10-22 [1] Bioconductor
+#>  spatialLIBD          * 1.17.9    2024-10-22 [1] Bioconductor
 #>  statmod                1.5.0     2023-01-06 [1] RSPM (R 4.4.0)
 #>  stringi                1.8.4     2024-05-06 [2] RSPM (R 4.4.0)
 #>  stringr                1.5.1     2023-11-14 [2] RSPM (R 4.4.0)
diff --git a/articles/guide_to_spatial_registration.html b/articles/guide_to_spatial_registration.html
index 0d0a27b4..83fc07ba 100644
--- a/articles/guide_to_spatial_registration.html
+++ b/articles/guide_to_spatial_registration.html
@@ -39,7 +39,7 @@
       
       
         spatialLIBD
-        1.17.8
+        1.17.9
       
     
 
@@ -288,7 +288,7 @@ 
Spatial Reference
 ## get reference layer enrichment statistics
 layer_modeling_results <- fetch_data(type = "modeling_results")
-#> 2024-10-22 13:37:09.185135 loading file /github/home/.cache/R/BiocFileCache/123837aa8e57_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
+#> 2024-10-22 13:41:24.006346 loading file /github/home/.cache/R/BiocFileCache/12397eec449a_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
 
 layer_modeling_results$enrichment[1:5, 1:5]
 #>    t_stat_WM t_stat_Layer1 t_stat_Layer2 t_stat_Layer3 t_stat_Layer4
@@ -391,18 +391,18 @@ 
Get Enrichment statistics
     gene_ensembl = "gene_id",
     gene_name = "gene_name"
 )
-#> 2024-10-22 13:37:17.209186 make pseudobulk object
-#> 2024-10-22 13:37:18.917753 dropping 13 pseudo-bulked samples that are below 'min_ncells'.
-#> 2024-10-22 13:37:18.983305 drop lowly expressed genes
-#> 2024-10-22 13:37:19.150156 normalize expression
-#> 2024-10-22 13:37:20.668368 create model matrix
-#> 2024-10-22 13:37:20.692453 run duplicateCorrelation()
-#> 2024-10-22 13:37:33.890002 The estimated correlation is: 0.138734774807097
-#> 2024-10-22 13:37:33.892731 computing enrichment statistics
-#> 2024-10-22 13:37:35.100186 extract and reformat enrichment results
-#> 2024-10-22 13:37:35.156374 running the baseline pairwise model
-#> 2024-10-22 13:37:35.298604 computing pairwise statistics
-#> 2024-10-22 13:37:36.682248 computing F-statistics

+#> 2024-10-22 13:41:31.641899 make pseudobulk object
+#> 2024-10-22 13:41:33.338713 dropping 13 pseudo-bulked samples that are below 'min_ncells'.
+#> 2024-10-22 13:41:33.396399 drop lowly expressed genes
+#> 2024-10-22 13:41:33.565537 normalize expression
+#> 2024-10-22 13:41:35.055342 create model matrix
+#> 2024-10-22 13:41:35.079233 run duplicateCorrelation()
+#> 2024-10-22 13:41:48.088797 The estimated correlation is: 0.138734774807097
+#> 2024-10-22 13:41:48.091498 computing enrichment statistics
+#> 2024-10-22 13:41:49.242692 extract and reformat enrichment results
+#> 2024-10-22 13:41:49.297468 running the baseline pairwise model
+#> 2024-10-22 13:41:49.436564 computing pairwise statistics
+#> 2024-10-22 13:41:50.800792 computing F-statistics

Extract Enrichment t-statistics @@ -562,9 +562,9 @@

Reproducibilitylibrary("knitr") knit("guide_to_spatial_registration.Rmd", tangle = TRUE)

Date the vignette was generated.

-
#> [1] "2024-10-22 13:37:38 UTC"
+
#> [1] "2024-10-22 13:41:52 UTC"

Wallclock time spent generating the vignette.

-
#> Time difference of 41.795 secs
+
#> Time difference of 41.011 secs

R session information.

#> ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
 #>  setting  value
@@ -716,7 +716,7 @@ 
Reproducibility#>  SparseArray            1.4.8     2024-05-24 [1] Bioconductor 3.19 (R 4.4.1)
 #>  sparseMatrixStats      1.16.0    2024-04-30 [1] Bioconductor 3.19 (R 4.4.1)
 #>  SpatialExperiment    * 1.14.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.1)
-#>  spatialLIBD          * 1.17.8    2024-10-22 [1] Bioconductor
+#>  spatialLIBD          * 1.17.9    2024-10-22 [1] Bioconductor
 #>  statmod                1.5.0     2023-01-06 [1] RSPM (R 4.4.0)
 #>  stringi                1.8.4     2024-05-06 [2] RSPM (R 4.4.0)
 #>  stringr                1.5.1     2023-11-14 [2] RSPM (R 4.4.0)
diff --git a/articles/index.html b/articles/index.html
index f6caf708..615d5f48 100644
--- a/articles/index.html
+++ b/articles/index.html
@@ -17,7 +17,7 @@
       
       
         spatialLIBD
-        1.17.8
+        1.17.9
       
     
 
diff --git a/articles/multi_gene_plots.html b/articles/multi_gene_plots.html
index d61208f3..b93afcfd 100644
--- a/articles/multi_gene_plots.html
+++ b/articles/multi_gene_plots.html
@@ -39,7 +39,7 @@
       
       
         spatialLIBD
-        1.17.8
+        1.17.9
       
     
 
@@ -195,9 +195,9 @@ 
Plotting One Gene
 modeling_results <- fetch_data(type = "modeling_results")
-#> 2024-10-22 13:38:03.175224 loading file /github/home/.cache/R/BiocFileCache/123837aa8e57_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
+#> 2024-10-22 13:42:16.814237 loading file /github/home/.cache/R/BiocFileCache/12397eec449a_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
 sce_layer <- fetch_data(type = "sce_layer")
-#> 2024-10-22 13:38:04.076334 loading file /github/home/.cache/R/BiocFileCache/123855dc376b_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-10-22 13:42:18.055795 loading file /github/home/.cache/R/BiocFileCache/123965771ab_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
 sig_genes <- sig_genes_extract_all(
     n = 400,
     modeling_results = modeling_results,
@@ -421,9 +421,9 @@ 
Reproducibilitylibrary("knitr")
 knit("multi_gene_plots.Rmd", tangle = TRUE)

 
Date the vignette was generated.

-
#> [1] "2024-10-22 13:38:20 UTC"

+
#> [1] "2024-10-22 13:42:34 UTC"

 
Wallclock time spent generating the vignette.

-
#> Time difference of 36.838 secs

+
#> Time difference of 38.093 secs

 
R session information.

 
#> ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
 #>  setting  value
@@ -577,7 +577,7 @@ 
Reproducibility#>  SparseArray            1.4.8     2024-05-24 [1] Bioconductor 3.19 (R 4.4.1)
 #>  sparseMatrixStats      1.16.0    2024-04-30 [1] Bioconductor 3.19 (R 4.4.1)
 #>  SpatialExperiment    * 1.14.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.1)
-#>  spatialLIBD          * 1.17.8    2024-10-22 [1] Bioconductor
+#>  spatialLIBD          * 1.17.9    2024-10-22 [1] Bioconductor
 #>  statmod                1.5.0     2023-01-06 [1] RSPM (R 4.4.0)
 #>  stringi                1.8.4     2024-05-06 [2] RSPM (R 4.4.0)
 #>  stringr                1.5.1     2023-11-14 [2] RSPM (R 4.4.0)
diff --git a/articles/spatialLIBD.html b/articles/spatialLIBD.html
index 91bc280e..4a7a2ae8 100644
--- a/articles/spatialLIBD.html
+++ b/articles/spatialLIBD.html
@@ -39,7 +39,7 @@
       
       
         spatialLIBD
-        1.17.8
+        1.17.9
       
     
 
@@ -414,7 +414,7 @@ 
Downloading the data with s
 
 ## Download the small example sce data
 sce <- fetch_data(type = "sce_example", eh = ehub)
-#> 2024-10-22 13:38:35.960609 loading file /github/home/.cache/R/BiocFileCache/123843e73411_sce_sub_for_vignette.Rdata%3Fdl%3D1
+#> 2024-10-22 13:42:50.399234 loading file /github/home/.cache/R/BiocFileCache/12397a7633bb_sce_sub_for_vignette.Rdata%3Fdl%3D1
 
 ## Convert to a SpatialExperiment object
 spe <- sce_to_spe(sce)
@@ -426,9 +426,9 @@ 
Downloading the data with s
 
 ## Query ExperimentHub and download the data
 if (!exists("sce_layer")) sce_layer <- fetch_data(type = "sce_layer", eh = ehub)
-#> 2024-10-22 13:38:40.904161 loading file /github/home/.cache/R/BiocFileCache/123855dc376b_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-10-22 13:42:56.651042 loading file /github/home/.cache/R/BiocFileCache/123965771ab_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
 modeling_results <- fetch_data("modeling_results", eh = ehub)
-#> 2024-10-22 13:38:41.370555 loading file /github/home/.cache/R/BiocFileCache/123837aa8e57_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1

+#> 2024-10-22 13:42:57.111858 loading file /github/home/.cache/R/BiocFileCache/12397eec449a_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1

 
Once you have downloaded the objects, we can explore them a little
 bit

 
@@ -501,7 +501,7 @@ 
Downloading the data with s
         )
 )
 #>    user  system elapsed 
-#>   9.285   0.375   9.704
+#>   9.169   0.384   9.569
 
 ## Explore the result
 class(sig_genes)
@@ -1377,9 +1377,9 @@ 
Reproducibilitylibrary("knitr")
 knit("spatialLIBD.Rmd", tangle = TRUE)

 
Date the vignette was generated.

-
#> [1] "2024-10-22 13:38:59 UTC"

+
#> [1] "2024-10-22 13:43:14 UTC"

 
Wallclock time spent generating the vignette.

-
#> Time difference of 35.656 secs

+
#> Time difference of 37.055 secs

 
R session information.

 
#> ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
 #>  setting  value
@@ -1533,7 +1533,7 @@ 
Reproducibility#>  SparseArray            1.4.8     2024-05-24 [1] Bioconductor 3.19 (R 4.4.1)
 #>  sparseMatrixStats      1.16.0    2024-04-30 [1] Bioconductor 3.19 (R 4.4.1)
 #>  SpatialExperiment    * 1.14.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.1)
-#>  spatialLIBD          * 1.17.8    2024-10-22 [1] Bioconductor
+#>  spatialLIBD          * 1.17.9    2024-10-22 [1] Bioconductor
 #>  statmod                1.5.0     2023-01-06 [1] RSPM (R 4.4.0)
 #>  stringi                1.8.4     2024-05-06 [2] RSPM (R 4.4.0)
 #>  stringr                1.5.1     2023-11-14 [2] RSPM (R 4.4.0)
diff --git a/authors.html b/authors.html
index ef93138c..a83fef95 100644
--- a/authors.html
+++ b/authors.html
@@ -17,7 +17,7 @@
       
       
         spatialLIBD
-        1.17.8
+        1.17.9
       
     
 
diff --git a/index.html b/index.html
index 7d89213c..6c1ecc65 100644
--- a/index.html
+++ b/index.html
@@ -41,7 +41,7 @@
       
       
         spatialLIBD
-        1.17.8
+        1.17.9
       
     
 
diff --git a/news/index.html b/news/index.html
index a34433f9..60b45067 100644
--- a/news/index.html
+++ b/news/index.html
@@ -17,7 +17,7 @@
       
       
         spatialLIBD
-        1.17.8
+        1.17.9
       
     
 
@@ -66,6 +66,12 @@ 
Changelog 

       Source: NEWS.md
     
 
+    

+
spatialLIBD 1.17.9

+
BUG FIXES

+

     

 
spatialLIBD 1.17.6

 
BUG FIXES

diff --git a/pkgdown.yml b/pkgdown.yml
index 3bf04f37..db0004fd 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -6,4 +6,4 @@ articles:
   multi_gene_plots: multi_gene_plots.html
   spatialLIBD: spatialLIBD.html
   TenX_data_download: TenX_data_download.html
-last_built: 2024-10-22T13:31Z
+last_built: 2024-10-22T13:35Z
diff --git a/reference/add10xVisiumAnalysis.html b/reference/add10xVisiumAnalysis.html
index cc6b4123..4c66b57c 100644
--- a/reference/add10xVisiumAnalysis.html
+++ b/reference/add10xVisiumAnalysis.html
@@ -19,7 +19,7 @@
       
       
         spatialLIBD
-        1.17.8
+        1.17.9
       
     

 
diff --git a/reference/add_images.html b/reference/add_images.html
index 6882e49d..66b9d67b 100644
--- a/reference/add_images.html
+++ b/reference/add_images.html
@@ -25,7 +25,7 @@
       
       
         spatialLIBD
-        1.17.8
+        1.17.9
       
     
 
@@ -165,29 +165,29 @@ 
Examples

         image_paths = c("151507" = "https://spatial-dlpfc.s3.us-east-2.amazonaws.com/images/151507_tissue_lowres_image.png")
     ))
 }
-#> 2024-10-22 13:31:24.444759 loading file /github/home/.cache/R/BiocFileCache/1d0868184ba3_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
-#> 2024-10-22 13:31:39.762336 adding image for sample 151507
-#> 2024-10-22 13:31:40.566131 adding image for sample 151508
+#> 2024-10-22 13:35:24.602191 loading file /github/home/.cache/R/BiocFileCache/1d067b86505d_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-10-22 13:35:40.309153 adding image for sample 151507
+#> 2024-10-22 13:35:41.80882 adding image for sample 151508
 #> Warning: No image was found for sample: 151508
-#> 2024-10-22 13:31:40.56688 adding image for sample 151509
+#> 2024-10-22 13:35:41.809595 adding image for sample 151509
 #> Warning: No image was found for sample: 151509
-#> 2024-10-22 13:31:40.567386 adding image for sample 151510
+#> 2024-10-22 13:35:41.810122 adding image for sample 151510
 #> Warning: No image was found for sample: 151510
-#> 2024-10-22 13:31:40.567862 adding image for sample 151669
+#> 2024-10-22 13:35:41.810643 adding image for sample 151669
 #> Warning: No image was found for sample: 151669
-#> 2024-10-22 13:31:40.568334 adding image for sample 151670
+#> 2024-10-22 13:35:41.811123 adding image for sample 151670
 #> Warning: No image was found for sample: 151670
-#> 2024-10-22 13:31:40.568804 adding image for sample 151671
+#> 2024-10-22 13:35:41.811623 adding image for sample 151671
 #> Warning: No image was found for sample: 151671
-#> 2024-10-22 13:31:40.569269 adding image for sample 151672
+#> 2024-10-22 13:35:41.812262 adding image for sample 151672
 #> Warning: No image was found for sample: 151672
-#> 2024-10-22 13:31:40.569736 adding image for sample 151673
+#> 2024-10-22 13:35:41.812776 adding image for sample 151673
 #> Warning: No image was found for sample: 151673
-#> 2024-10-22 13:31:40.570213 adding image for sample 151674
+#> 2024-10-22 13:35:41.813268 adding image for sample 151674
 #> Warning: No image was found for sample: 151674
-#> 2024-10-22 13:31:40.570678 adding image for sample 151675
+#> 2024-10-22 13:35:41.813751 adding image for sample 151675
 #> Warning: No image was found for sample: 151675
-#> 2024-10-22 13:31:40.57114 adding image for sample 151676
+#> 2024-10-22 13:35:41.814222 adding image for sample 151676
 #> Warning: No image was found for sample: 151676
 #> DataFrame with 13 rows and 4 columns
 #>       sample_id    image_id   data scaleFactor
diff --git a/reference/add_key.html b/reference/add_key.html
index d515810b..b20d456d 100644
--- a/reference/add_key.html
+++ b/reference/add_key.html
@@ -19,7 +19,7 @@
       
       
         spatialLIBD
-        1.17.8
+        1.17.9
       
     
 
@@ -124,7 +124,7 @@ 
Examples

     spe$key_original <- NULL
     head(spe$key)
 }
-#> 2024-10-22 13:31:42.987489 loading file /github/home/.cache/R/BiocFileCache/1d0868184ba3_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-10-22 13:35:44.676045 loading file /github/home/.cache/R/BiocFileCache/1d067b86505d_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
 #> [1] "151507_AAACAACGAATAGTTC-1" "151507_AAACAAGTATCTCCCA-1"
 #> [3] "151507_AAACAATCTACTAGCA-1" "151507_AAACACCAATAACTGC-1"
 #> [5] "151507_AAACAGCTTTCAGAAG-1" "151507_AAACAGGGTCTATATT-1"
diff --git a/reference/add_qc_metrics.html b/reference/add_qc_metrics.html
index 4e806bc8..dd173e84 100644
--- a/reference/add_qc_metrics.html
+++ b/reference/add_qc_metrics.html
@@ -21,7 +21,7 @@
       
       
         spatialLIBD
-        1.17.8
+        1.17.9
       
     
 
@@ -144,7 +144,7 @@ 
Author

     
Examples

     
## Obtain the necessary data
 spe_pre_qc <- fetch_data("spatialDLPFC_Visium_example_subset")
-#> 2024-10-22 13:31:59.427832 loading file /github/home/.cache/R/BiocFileCache/123820e4f38e_spatialDLPFC_spe_subset_example.rds%3Fdl%3D1
+#> 2024-10-22 13:35:59.799945 loading file /github/home/.cache/R/BiocFileCache/12393a6df46_spatialDLPFC_spe_subset_example.rds%3Fdl%3D1
 
 ## For now, we fake out tissue spots in example data
 spe_qc <- spe_pre_qc
diff --git a/reference/annotate_registered_clusters.html b/reference/annotate_registered_clusters.html
index 1518a7ed..2fca464c 100644
--- a/reference/annotate_registered_clusters.html
+++ b/reference/annotate_registered_clusters.html
@@ -21,7 +21,7 @@
       
       
         spatialLIBD
-        1.17.8
+        1.17.9
       
     

 
@@ -137,7 +137,7 @@ 
Examples

 if (!exists("modeling_results")) {
     modeling_results <- fetch_data(type = "modeling_results")
 }
-#> 2024-10-22 13:32:11.6198 loading file /github/home/.cache/R/BiocFileCache/123837aa8e57_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
+#> 2024-10-22 13:36:12.32106 loading file /github/home/.cache/R/BiocFileCache/12397eec449a_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
 
 ## Compute the correlations
 cor_stats_layer <- layer_stat_cor(
diff --git a/reference/check_modeling_results.html b/reference/check_modeling_results.html
index 74f7ec8f..96ec3b9a 100644
--- a/reference/check_modeling_results.html
+++ b/reference/check_modeling_results.html
@@ -18,7 +18,7 @@
       
       
         spatialLIBD
-        1.17.8
+        1.17.9
       
     
 
@@ -108,7 +108,7 @@ 
Examples

 if (!exists("modeling_results")) {
     modeling_results <- fetch_data(type = "modeling_results")
 }
-#> 2024-10-22 13:32:12.746485 loading file /github/home/.cache/R/BiocFileCache/123837aa8e57_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
+#> 2024-10-22 13:36:13.712153 loading file /github/home/.cache/R/BiocFileCache/12397eec449a_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
 
 ## Check the object
 xx <- check_modeling_results(modeling_results)
diff --git a/reference/check_sce.html b/reference/check_sce.html
index 6cb76fbc..2f176156 100644
--- a/reference/check_sce.html
+++ b/reference/check_sce.html
@@ -20,7 +20,7 @@
       
       
         spatialLIBD
-        1.17.8
+        1.17.9
       
     
 
@@ -131,7 +131,7 @@ 
Examples

     ## Check the object
     check_sce(sce_example)
 }
-#> 2024-10-22 13:32:13.932401 loading file /github/home/.cache/R/BiocFileCache/123843e73411_sce_sub_for_vignette.Rdata%3Fdl%3D1
+#> 2024-10-22 13:36:15.088958 loading file /github/home/.cache/R/BiocFileCache/12397a7633bb_sce_sub_for_vignette.Rdata%3Fdl%3D1
 #> class: SingleCellExperiment 
 #> dim: 33538 47681 
 #> metadata(1): image
diff --git a/reference/check_sce_layer.html b/reference/check_sce_layer.html
index f2d6a1f5..9e0337c3 100644
--- a/reference/check_sce_layer.html
+++ b/reference/check_sce_layer.html
@@ -18,7 +18,7 @@
       
       
         spatialLIBD
-        1.17.8
+        1.17.9
       
     
 
@@ -112,7 +112,7 @@ 
Examples

 ## Obtain example data from the HumanPilot project
 ## (Maynard, Collado-Torres, et al, 2021)
 if (!exists("sce_layer")) sce_layer <- fetch_data("sce_layer")
-#> 2024-10-22 13:32:16.458107 loading file /github/home/.cache/R/BiocFileCache/123855dc376b_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-10-22 13:36:17.798803 loading file /github/home/.cache/R/BiocFileCache/123965771ab_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
 
 ## Check the pseudo-bulked data
 check_sce_layer(sce_layer)
diff --git a/reference/check_spe.html b/reference/check_spe.html
index 7d53eb4c..870199f4 100644
--- a/reference/check_spe.html
+++ b/reference/check_spe.html
@@ -18,7 +18,7 @@
       
       
         spatialLIBD
-        1.17.8
+        1.17.9
       
     
 
@@ -123,7 +123,7 @@ 
Examples

     ## Check the object
     check_spe(spe)
 }
-#> 2024-10-22 13:32:17.717738 loading file /github/home/.cache/R/BiocFileCache/1d0868184ba3_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-10-22 13:36:19.352998 loading file /github/home/.cache/R/BiocFileCache/1d067b86505d_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
 #> class: SpatialExperiment 
 #> dim: 33538 47681 
 #> metadata(0):
diff --git a/reference/cluster_export.html b/reference/cluster_export.html
index a79ada35..0f3db193 100644
--- a/reference/cluster_export.html
+++ b/reference/cluster_export.html
@@ -21,7 +21,7 @@
       
       
         spatialLIBD
-        1.17.8
+        1.17.9
       
     
 
@@ -134,7 +134,7 @@ 
Examples

     cluster_export(spe, "spatialLIBD")
     cluster_export(spe, "GraphBased")
 }
-#> 2024-10-22 13:32:32.231737 loading file /github/home/.cache/R/BiocFileCache/1d0868184ba3_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-10-22 13:36:34.716348 loading file /github/home/.cache/R/BiocFileCache/1d067b86505d_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
 #> Overwriting 'spe$key'. Set 'overwrite = FALSE' if you do not want to overwrite it.
 #> Overwriting 'spe$key'. Set 'overwrite = FALSE' if you do not want to overwrite it.
 

diff --git a/reference/cluster_import.html b/reference/cluster_import.html
index d7db8bb3..3cf6cdb2 100644
--- a/reference/cluster_import.html
+++ b/reference/cluster_import.html
@@ -20,7 +20,7 @@
       
       
         spatialLIBD
-        1.17.8
+        1.17.9
       
     
 
@@ -137,11 +137,11 @@ 
Examples

     ## Re-import them
     colData(cluster_import(spe))
 }
-#> 2024-10-22 13:32:47.335735 loading file /github/home/.cache/R/BiocFileCache/1d0868184ba3_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-10-22 13:36:50.383511 loading file /github/home/.cache/R/BiocFileCache/1d067b86505d_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
 #> Overwriting 'spe$key'. Set 'overwrite = FALSE' if you do not want to overwrite it.
-#> Warning: '/tmp/RtmpGn3TQR/exported_clusters/spatialLIBD' already exists
+#> Warning: '/tmp/RtmptGdw7c/exported_clusters/spatialLIBD' already exists
 #> Overwriting 'spe$key'. Set 'overwrite = FALSE' if you do not want to overwrite it.
-#> Warning: '/tmp/RtmpGn3TQR/exported_clusters/GraphBased' already exists
+#> Warning: '/tmp/RtmptGdw7c/exported_clusters/GraphBased' already exists
 #> Overwriting 'spe$key'. Set 'overwrite = FALSE' if you do not want to overwrite it.
 #> DataFrame with 47681 rows and 71 columns
 #>                                       key   sample_id   Cluster   sum_umi
diff --git a/reference/enough_ram.html b/reference/enough_ram.html
index 680f859b..0f1f8b7d 100644
--- a/reference/enough_ram.html
+++ b/reference/enough_ram.html
@@ -17,7 +17,7 @@
       
       
         spatialLIBD
-        1.17.8
+        1.17.9
       
     
 
diff --git a/reference/fetch_data.html b/reference/fetch_data.html
index 6e3ab431..3f75ed5f 100644
--- a/reference/fetch_data.html
+++ b/reference/fetch_data.html
@@ -25,7 +25,7 @@
       
       
         spatialLIBD
-        1.17.8
+        1.17.9
       
     
 
@@ -166,7 +166,7 @@ 
Examples

 ## Download the SingleCellExperiment object
 ## at the layer-level
 if (!exists("sce_layer")) sce_layer <- fetch_data("sce_layer")
-#> 2024-10-22 13:33:02.491858 loading file /github/home/.cache/R/BiocFileCache/123855dc376b_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-10-22 13:37:06.236033 loading file /github/home/.cache/R/BiocFileCache/123965771ab_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
 
 ## Explore the data
 sce_layer
diff --git a/reference/frame_limits.html b/reference/frame_limits.html
index a7b174e9..5d1a9f55 100644
--- a/reference/frame_limits.html
+++ b/reference/frame_limits.html
@@ -27,7 +27,7 @@
       
       
         spatialLIBD
-        1.17.8
+        1.17.9
       
     
 
@@ -154,7 +154,7 @@ 
Examples

     ## Obtain the frame limits for one sample
     frame_limits(spe, sampleid = "151673")
 }
-#> 2024-10-22 13:33:04.197396 loading file /github/home/.cache/R/BiocFileCache/1d0868184ba3_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-10-22 13:37:08.260365 loading file /github/home/.cache/R/BiocFileCache/1d067b86505d_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
 #> $y_min
 #> [1] 64
 #> 
diff --git a/reference/gene_set_enrichment.html b/reference/gene_set_enrichment.html
index be7d40db..6b96248e 100644
--- a/reference/gene_set_enrichment.html
+++ b/reference/gene_set_enrichment.html
@@ -22,7 +22,7 @@
       
       
         spatialLIBD
-        1.17.8
+        1.17.9
       
     
 
@@ -176,7 +176,7 @@ 
Examples

 if (!exists("modeling_results")) {
     modeling_results <- fetch_data(type = "modeling_results")
 }
-#> 2024-10-22 13:33:19.074355 loading file /github/home/.cache/R/BiocFileCache/123837aa8e57_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
+#> 2024-10-22 13:37:22.992435 loading file /github/home/.cache/R/BiocFileCache/12397eec449a_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
 
 ## Compute the gene set enrichment results
 asd_sfari_enrichment <- gene_set_enrichment(
diff --git a/reference/gene_set_enrichment_plot.html b/reference/gene_set_enrichment_plot.html
index 220031aa..1c57bd55 100644
--- a/reference/gene_set_enrichment_plot.html
+++ b/reference/gene_set_enrichment_plot.html
@@ -18,7 +18,7 @@
       
       
         spatialLIBD
-        1.17.8
+        1.17.9
       
     
 
@@ -178,7 +178,7 @@ 
Examples

 if (!exists("modeling_results")) {
     modeling_results <- fetch_data(type = "modeling_results")
 }
-#> 2024-10-22 13:33:20.449053 loading file /github/home/.cache/R/BiocFileCache/123837aa8e57_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
+#> 2024-10-22 13:37:24.664073 loading file /github/home/.cache/R/BiocFileCache/12397eec449a_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
 
 ## Compute the gene set enrichment results
 asd_sfari_enrichment <- gene_set_enrichment(
diff --git a/reference/geom_spatial.html b/reference/geom_spatial.html
index 742878c0..40cb8101 100644
--- a/reference/geom_spatial.html
+++ b/reference/geom_spatial.html
@@ -20,7 +20,7 @@
       
       
         spatialLIBD
-        1.17.8
+        1.17.9
       
     
 
@@ -175,7 +175,7 @@ 
Examples

     ## Clean up
     rm(spe_sub)
 }
-#> 2024-10-22 13:33:22.291924 loading file /github/home/.cache/R/BiocFileCache/1d0868184ba3_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-10-22 13:37:26.675108 loading file /github/home/.cache/R/BiocFileCache/1d067b86505d_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
diff --git a/reference/get_colors.html b/reference/get_colors.html index 17060b52..7e003b88 100644 --- a/reference/get_colors.html +++ b/reference/get_colors.html @@ -18,7 +18,7 @@ spatialLIBD - 1.17.8 + 1.17.9 @@ -105,7 +105,7 @@

Examples


 ## Obtain the necessary data
 if (!exists("sce_layer")) sce_layer <- fetch_data("sce_layer")
-#> 2024-10-22 13:33:37.40249 loading file /github/home/.cache/R/BiocFileCache/123855dc376b_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-10-22 13:37:45.234123 loading file /github/home/.cache/R/BiocFileCache/123965771ab_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
 
 ## Example layer colors with the corresponding names
 get_colors(libd_layer_colors, sce_layer$layer_guess)
diff --git a/reference/img_edit.html b/reference/img_edit.html
index 76484840..1f3662f6 100644
--- a/reference/img_edit.html
+++ b/reference/img_edit.html
@@ -19,7 +19,7 @@
       
       
         spatialLIBD
-        1.17.8
+        1.17.9
@@ -222,7 +222,7 @@

Examples

x <- img_edit(spe, sampleid = "151507", brightness = 25) plot(x) } -#> 2024-10-22 13:33:38.612079 loading file /github/home/.cache/R/BiocFileCache/1d0868184ba3_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-10-22 13:37:46.800305 loading file /github/home/.cache/R/BiocFileCache/1d067b86505d_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 diff --git a/reference/img_update.html b/reference/img_update.html index d8704231..97587f3d 100644 --- a/reference/img_update.html +++ b/reference/img_update.html @@ -17,7 +17,7 @@ spatialLIBD - 1.17.8 + 1.17.9 @@ -139,7 +139,7 @@

Examples

## Reduce brightness to 25% and update the imgData() imgData(img_update(spe, sampleid = "151507", brightness = 25)) } -#> 2024-10-22 13:33:53.992117 loading file /github/home/.cache/R/BiocFileCache/1d0868184ba3_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-10-22 13:38:02.861559 loading file /github/home/.cache/R/BiocFileCache/1d067b86505d_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 #> DataFrame with 13 rows and 4 columns #> sample_id image_id data scaleFactor #> <character> <character> <list> <numeric> diff --git a/reference/img_update_all.html b/reference/img_update_all.html index 12d2ee0e..ede3cac1 100644 --- a/reference/img_update_all.html +++ b/reference/img_update_all.html @@ -19,7 +19,7 @@ spatialLIBD - 1.17.8 + 1.17.9 @@ -138,7 +138,7 @@

Examples

## update the imgData() imgData(img_update_all(spe, brightness = 25)) } -#> 2024-10-22 13:34:08.04101 loading file /github/home/.cache/R/BiocFileCache/1d0868184ba3_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-10-22 13:38:17.499327 loading file /github/home/.cache/R/BiocFileCache/1d067b86505d_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 #> DataFrame with 24 rows and 4 columns #> sample_id image_id data scaleFactor #> <character> <character> <list> <numeric> diff --git a/reference/index.html b/reference/index.html index e3dc0f1e..2c4f9884 100644 --- a/reference/index.html +++ b/reference/index.html @@ -17,7 +17,7 @@ spatialLIBD - 1.17.8 + 1.17.9 diff --git a/reference/layer_boxplot.html b/reference/layer_boxplot.html index bfb4466b..58cf7170 100644 --- a/reference/layer_boxplot.html +++ b/reference/layer_boxplot.html @@ -19,7 +19,7 @@ spatialLIBD - 1.17.8 + 1.17.9 @@ -185,9 +185,9 @@

Examples

if (!exists("modeling_results")) { modeling_results <- fetch_data(type = "modeling_results") } -#> 2024-10-22 13:34:24.546839 loading file /github/home/.cache/R/BiocFileCache/123837aa8e57_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1 +#> 2024-10-22 13:38:34.960591 loading file /github/home/.cache/R/BiocFileCache/12397eec449a_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1 if (!exists("sce_layer")) sce_layer <- fetch_data(type = "sce_layer") -#> 2024-10-22 13:34:25.486094 loading file /github/home/.cache/R/BiocFileCache/123855dc376b_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-10-22 13:38:36.250165 loading file /github/home/.cache/R/BiocFileCache/123965771ab_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1 ## Top 2 genes from the enrichment model sig_genes <- sig_genes_extract_all( diff --git a/reference/layer_matrix_plot.html b/reference/layer_matrix_plot.html index 52acebe8..d2dcf995 100644 --- a/reference/layer_matrix_plot.html +++ b/reference/layer_matrix_plot.html @@ -20,7 +20,7 @@ spatialLIBD - 1.17.8 + 1.17.9 diff --git a/reference/layer_stat_cor.html b/reference/layer_stat_cor.html index 7265d113..22db6cd0 100644 --- a/reference/layer_stat_cor.html +++ b/reference/layer_stat_cor.html @@ -17,7 +17,7 @@ spatialLIBD - 1.17.8 + 1.17.9 @@ -156,7 +156,7 @@

Examples

if (!exists("modeling_results")) { modeling_results <- fetch_data(type = "modeling_results") } -#> 2024-10-22 13:34:28.745313 loading file /github/home/.cache/R/BiocFileCache/123837aa8e57_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1 +#> 2024-10-22 13:38:39.933834 loading file /github/home/.cache/R/BiocFileCache/12397eec449a_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1 ## Compute the correlations cor_stats_layer <- layer_stat_cor( diff --git a/reference/layer_stat_cor_plot.html b/reference/layer_stat_cor_plot.html index 39532483..9fe85577 100644 --- a/reference/layer_stat_cor_plot.html +++ b/reference/layer_stat_cor_plot.html @@ -20,7 +20,7 @@ spatialLIBD - 1.17.8 + 1.17.9 @@ -145,7 +145,7 @@

Examples

if (!exists("modeling_results")) { modeling_results <- fetch_data(type = "modeling_results") } -#> 2024-10-22 13:34:29.862691 loading file /github/home/.cache/R/BiocFileCache/123837aa8e57_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1 +#> 2024-10-22 13:38:41.365265 loading file /github/home/.cache/R/BiocFileCache/12397eec449a_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1 ## Compute the correlations cor_stats_layer <- layer_stat_cor( diff --git a/reference/libd_layer_colors.html b/reference/libd_layer_colors.html index 85f1ddde..fd0c4e9c 100644 --- a/reference/libd_layer_colors.html +++ b/reference/libd_layer_colors.html @@ -18,7 +18,7 @@ spatialLIBD - 1.17.8 + 1.17.9 diff --git a/reference/locate_images.html b/reference/locate_images.html index 3b90b9d0..5f59a3a6 100644 --- a/reference/locate_images.html +++ b/reference/locate_images.html @@ -19,7 +19,7 @@ spatialLIBD - 1.17.8 + 1.17.9 diff --git a/reference/multi_gene_pca.html b/reference/multi_gene_pca.html index c653337d..f4957fb3 100644 --- a/reference/multi_gene_pca.html +++ b/reference/multi_gene_pca.html @@ -22,7 +22,7 @@ spatialLIBD - 1.17.8 + 1.17.9 diff --git a/reference/multi_gene_sparsity.html b/reference/multi_gene_sparsity.html index eedc3913..a256ceaf 100644 --- a/reference/multi_gene_sparsity.html +++ b/reference/multi_gene_sparsity.html @@ -18,7 +18,7 @@ spatialLIBD - 1.17.8 + 1.17.9 diff --git a/reference/multi_gene_z_score.html b/reference/multi_gene_z_score.html index 263317fe..988ee1c4 100644 --- a/reference/multi_gene_z_score.html +++ b/reference/multi_gene_z_score.html @@ -18,7 +18,7 @@ spatialLIBD - 1.17.8 + 1.17.9 diff --git a/reference/prep_stitched_data.html b/reference/prep_stitched_data.html index b1d08743..dcbbf68f 100644 --- a/reference/prep_stitched_data.html +++ b/reference/prep_stitched_data.html @@ -22,7 +22,7 @@ spatialLIBD - 1.17.8 + 1.17.9 diff --git a/reference/read10xVisiumAnalysis.html b/reference/read10xVisiumAnalysis.html index e3753c55..7dfaf821 100644 --- a/reference/read10xVisiumAnalysis.html +++ b/reference/read10xVisiumAnalysis.html @@ -18,7 +18,7 @@ spatialLIBD - 1.17.8 + 1.17.9 diff --git a/reference/read10xVisiumWrapper.html b/reference/read10xVisiumWrapper.html index ce3f71f2..46cca669 100644 --- a/reference/read10xVisiumWrapper.html +++ b/reference/read10xVisiumWrapper.html @@ -20,7 +20,7 @@ spatialLIBD - 1.17.8 + 1.17.9 diff --git a/reference/registration_block_cor.html b/reference/registration_block_cor.html index db648eed..55170518 100644 --- a/reference/registration_block_cor.html +++ b/reference/registration_block_cor.html @@ -20,7 +20,7 @@ spatialLIBD - 1.17.8 + 1.17.9 @@ -146,9 +146,9 @@

Examples

#> #> rgstr_> ## Pseudo-bulk #> rgstr_> sce_pseudo <- registration_pseudobulk(sce, "Cell_Cycle", "sample_id", c("age"), min_ncells = NULL) -#> 2024-10-22 13:34:32.927881 make pseudobulk object -#> 2024-10-22 13:34:33.138093 drop lowly expressed genes -#> 2024-10-22 13:34:33.208394 normalize expression +#> 2024-10-22 13:38:44.463403 make pseudobulk object +#> 2024-10-22 13:38:44.63967 drop lowly expressed genes +#> 2024-10-22 13:38:44.7071 normalize expression #> #> rgstr_> colData(sce_pseudo) #> DataFrame with 20 rows and 8 columns @@ -180,7 +180,7 @@

Examples

#> E_S S E 11 #> #> rgstr_> registration_mod <- registration_model(sce_pseudo, "age") -#> 2024-10-22 13:34:33.287393 create model matrix +#> 2024-10-22 13:38:44.791921 create model matrix #> #> rgstr_> head(registration_mod) #> registration_variableG0 registration_variableG1 registration_variableG2M @@ -198,8 +198,8 @@

Examples

#> E_G0 0 20.97006 #> A_G1 0 19.18719 block_cor <- registration_block_cor(sce_pseudo, registration_mod) -#> 2024-10-22 13:34:33.300276 run duplicateCorrelation() -#> 2024-10-22 13:34:34.570867 The estimated correlation is: -0.0187869166526901 +#> 2024-10-22 13:38:44.833633 run duplicateCorrelation() +#> 2024-10-22 13:38:46.092836 The estimated correlation is: -0.0187869166526901 diff --git a/reference/registration_model.html b/reference/registration_model.html index 1cd9c7e3..89013347 100644 --- a/reference/registration_model.html +++ b/reference/registration_model.html @@ -21,7 +21,7 @@ spatialLIBD - 1.17.8 + 1.17.9 @@ -148,9 +148,9 @@

Examples

#> #> rgstr_> ## Pseudo-bulk #> rgstr_> sce_pseudo <- registration_pseudobulk(sce, "Cell_Cycle", "sample_id", c("age"), min_ncells = NULL) -#> 2024-10-22 13:34:35.002752 make pseudobulk object -#> 2024-10-22 13:34:35.190035 drop lowly expressed genes -#> 2024-10-22 13:34:35.244808 normalize expression +#> 2024-10-22 13:38:46.488082 make pseudobulk object +#> 2024-10-22 13:38:46.669905 drop lowly expressed genes +#> 2024-10-22 13:38:46.723507 normalize expression #> #> rgstr_> colData(sce_pseudo) #> DataFrame with 20 rows and 8 columns @@ -181,7 +181,7 @@

Examples

#> D_S S D 14 #> E_S S E 11 registration_mod <- registration_model(sce_pseudo, "age") -#> 2024-10-22 13:34:35.321421 create model matrix +#> 2024-10-22 13:38:46.824717 create model matrix head(registration_mod) #> registration_variableG0 registration_variableG1 registration_variableG2M #> A_G0 1 0 0 diff --git a/reference/registration_pseudobulk.html b/reference/registration_pseudobulk.html index f2cea56a..c4c885e9 100644 --- a/reference/registration_pseudobulk.html +++ b/reference/registration_pseudobulk.html @@ -18,7 +18,7 @@ spatialLIBD - 1.17.8 + 1.17.9 @@ -159,9 +159,9 @@

Examples

## Pseudo-bulk sce_pseudo <- registration_pseudobulk(sce, "Cell_Cycle", "sample_id", c("age"), min_ncells = NULL) -#> 2024-10-22 13:34:35.745105 make pseudobulk object -#> 2024-10-22 13:34:35.940542 drop lowly expressed genes -#> 2024-10-22 13:34:35.995279 normalize expression +#> 2024-10-22 13:38:47.230213 make pseudobulk object +#> 2024-10-22 13:38:47.381068 drop lowly expressed genes +#> 2024-10-22 13:38:47.433867 normalize expression colData(sce_pseudo) #> DataFrame with 20 rows and 8 columns #> Mutation_Status Cell_Cycle Treatment sample_id age diff --git a/reference/registration_stats_anova.html b/reference/registration_stats_anova.html index 3089779b..c3595fc8 100644 --- a/reference/registration_stats_anova.html +++ b/reference/registration_stats_anova.html @@ -20,7 +20,7 @@ spatialLIBD - 1.17.8 + 1.17.9 @@ -180,9 +180,9 @@

Examples

#> #> rgstr_> ## Pseudo-bulk #> rgstr_> sce_pseudo <- registration_pseudobulk(sce, "Cell_Cycle", "sample_id", c("age"), min_ncells = NULL) -#> 2024-10-22 13:34:36.589667 make pseudobulk object -#> 2024-10-22 13:34:36.745527 drop lowly expressed genes -#> 2024-10-22 13:34:36.80442 normalize expression +#> 2024-10-22 13:38:48.034281 make pseudobulk object +#> 2024-10-22 13:38:48.183998 drop lowly expressed genes +#> 2024-10-22 13:38:48.23717 normalize expression #> #> rgstr_> colData(sce_pseudo) #> DataFrame with 20 rows and 8 columns @@ -214,7 +214,7 @@

Examples

#> E_S S E 11 #> #> rgstr_> registration_mod <- registration_model(sce_pseudo, "age") -#> 2024-10-22 13:34:36.883524 create model matrix +#> 2024-10-22 13:38:48.310268 create model matrix #> #> rgstr_> head(registration_mod) #> registration_variableG0 registration_variableG1 registration_variableG2M @@ -233,13 +233,13 @@

Examples

#> A_G1 0 19.18719 #> #> rgst__> block_cor <- registration_block_cor(sce_pseudo, registration_mod) -#> 2024-10-22 13:34:36.895432 run duplicateCorrelation() -#> 2024-10-22 13:34:38.214723 The estimated correlation is: -0.0187869166526901 +#> 2024-10-22 13:38:48.321711 run duplicateCorrelation() +#> 2024-10-22 13:38:49.573632 The estimated correlation is: -0.0187869166526901 results_anova <- registration_stats_anova(sce_pseudo, block_cor, "age", gene_ensembl = "ensembl", gene_name = "gene_name", suffix = "example" ) -#> 2024-10-22 13:34:38.227669 computing F-statistics +#> 2024-10-22 13:38:49.586039 computing F-statistics head(results_anova) #> f_stat_example p_value_example fdr_example AveExpr_example ensembl gene #> 1 0.1328075 0.93918553 0.9951876 5.499488 ENSG1 gene1 @@ -254,7 +254,7 @@

Examples

block_cor = NaN, "age", gene_ensembl = "ensembl", gene_name = "gene_name", suffix = "example" ) -#> 2024-10-22 13:34:38.29041 computing F-statistics +#> 2024-10-22 13:38:49.647101 computing F-statistics head(results_anova_nan) #> f_stat_example p_value_example fdr_example AveExpr_example ensembl gene #> 1 0.1357180 0.93736053 0.9943765 5.499488 ENSG1 gene1 @@ -276,7 +276,7 @@

Examples

covars = NULL, gene_ensembl = "ensembl", gene_name = "gene_name", suffix = "nocovar" ) -#> 2024-10-22 13:34:38.339799 computing F-statistics +#> 2024-10-22 13:38:49.696167 computing F-statistics head(results_anova_nocovar) #> f_stat_nocovar p_value_nocovar fdr_nocovar AveExpr_nocovar ensembl gene #> 1 0.1393641 0.9351345 0.9962097 5.499488 ENSG1 gene1 diff --git a/reference/registration_stats_enrichment.html b/reference/registration_stats_enrichment.html index 9cf765f5..3c48c35c 100644 --- a/reference/registration_stats_enrichment.html +++ b/reference/registration_stats_enrichment.html @@ -19,7 +19,7 @@ spatialLIBD - 1.17.8 + 1.17.9 @@ -171,9 +171,9 @@

Examples

#> #> rgstr_> ## Pseudo-bulk #> rgstr_> sce_pseudo <- registration_pseudobulk(sce, "Cell_Cycle", "sample_id", c("age"), min_ncells = NULL) -#> 2024-10-22 13:34:38.866167 make pseudobulk object -#> 2024-10-22 13:34:39.054213 drop lowly expressed genes -#> 2024-10-22 13:34:39.109378 normalize expression +#> 2024-10-22 13:38:50.244106 make pseudobulk object +#> 2024-10-22 13:38:50.394444 drop lowly expressed genes +#> 2024-10-22 13:38:50.447676 normalize expression #> #> rgstr_> colData(sce_pseudo) #> DataFrame with 20 rows and 8 columns @@ -205,7 +205,7 @@

Examples

#> E_S S E 11 #> #> rgstr_> registration_mod <- registration_model(sce_pseudo, "age") -#> 2024-10-22 13:34:39.184021 create model matrix +#> 2024-10-22 13:38:50.520319 create model matrix #> #> rgstr_> head(registration_mod) #> registration_variableG0 registration_variableG1 registration_variableG2M @@ -224,14 +224,14 @@

Examples

#> A_G1 0 19.18719 #> #> rgst__> block_cor <- registration_block_cor(sce_pseudo, registration_mod) -#> 2024-10-22 13:34:39.196029 run duplicateCorrelation() -#> 2024-10-22 13:34:40.476386 The estimated correlation is: -0.0187869166526901 +#> 2024-10-22 13:38:50.531584 run duplicateCorrelation() +#> 2024-10-22 13:38:51.786606 The estimated correlation is: -0.0187869166526901 results_enrichment <- registration_stats_enrichment(sce_pseudo, block_cor, "age", gene_ensembl = "ensembl", gene_name = "gene_name" ) -#> 2024-10-22 13:34:40.480113 computing enrichment statistics -#> 2024-10-22 13:34:40.600185 extract and reformat enrichment results +#> 2024-10-22 13:38:51.790061 computing enrichment statistics +#> 2024-10-22 13:38:51.946818 extract and reformat enrichment results head(results_enrichment) #> t_stat_G0 t_stat_G1 t_stat_G2M t_stat_S p_value_G0 p_value_G1 #> Gene_0001 0.1482017 0.5610669 -0.3612235 -0.3458508 0.88374480 0.58130631 @@ -260,8 +260,8 @@

Examples

block_cor = NaN, "age", gene_ensembl = "ensembl", gene_name = "gene_name" ) -#> 2024-10-22 13:34:40.634204 computing enrichment statistics -#> 2024-10-22 13:34:40.739086 extract and reformat enrichment results +#> 2024-10-22 13:38:51.980221 computing enrichment statistics +#> 2024-10-22 13:38:52.0804 extract and reformat enrichment results head(results_enrichment_nan) #> t_stat_G0 t_stat_G1 t_stat_G2M t_stat_S p_value_G0 p_value_G1 #> Gene_0001 0.1497747 0.56711100 -0.3650801 -0.3495404 0.88252049 0.57727506 diff --git a/reference/registration_stats_pairwise.html b/reference/registration_stats_pairwise.html index 14f8a3a3..01cae5f6 100644 --- a/reference/registration_stats_pairwise.html +++ b/reference/registration_stats_pairwise.html @@ -20,7 +20,7 @@ spatialLIBD - 1.17.8 + 1.17.9 @@ -173,9 +173,9 @@

Examples

#> #> rgstr_> ## Pseudo-bulk #> rgstr_> sce_pseudo <- registration_pseudobulk(sce, "Cell_Cycle", "sample_id", c("age"), min_ncells = NULL) -#> 2024-10-22 13:34:41.228732 make pseudobulk object -#> 2024-10-22 13:34:41.385726 drop lowly expressed genes -#> 2024-10-22 13:34:41.441598 normalize expression +#> 2024-10-22 13:38:52.519078 make pseudobulk object +#> 2024-10-22 13:38:52.669983 drop lowly expressed genes +#> 2024-10-22 13:38:52.723413 normalize expression #> #> rgstr_> colData(sce_pseudo) #> DataFrame with 20 rows and 8 columns @@ -207,7 +207,7 @@

Examples

#> E_S S E 11 #> #> rgstr_> registration_mod <- registration_model(sce_pseudo, "age") -#> 2024-10-22 13:34:41.517191 create model matrix +#> 2024-10-22 13:38:52.79751 create model matrix #> #> rgstr_> head(registration_mod) #> registration_variableG0 registration_variableG1 registration_variableG2M @@ -226,14 +226,14 @@

Examples

#> A_G1 0 19.18719 #> #> rgst__> block_cor <- registration_block_cor(sce_pseudo, registration_mod) -#> 2024-10-22 13:34:41.529041 run duplicateCorrelation() -#> 2024-10-22 13:34:42.847176 The estimated correlation is: -0.0187869166526901 +#> 2024-10-22 13:38:52.808987 run duplicateCorrelation() +#> 2024-10-22 13:38:54.094011 The estimated correlation is: -0.0187869166526901 results_pairwise <- registration_stats_pairwise(sce_pseudo, registration_mod, block_cor, gene_ensembl = "ensembl", gene_name = "gene_name" ) -#> 2024-10-22 13:34:42.849047 running the baseline pairwise model -#> 2024-10-22 13:34:42.866168 computing pairwise statistics +#> 2024-10-22 13:38:54.0958 running the baseline pairwise model +#> 2024-10-22 13:38:54.112657 computing pairwise statistics head(results_pairwise) #> t_stat_G0-G1 t_stat_G0-G2M t_stat_G0-S t_stat_G1-G2M t_stat_G1-S #> Gene_0001 -0.2393683 0.29771391 0.28880637 0.5370822 0.5281747 @@ -277,8 +277,8 @@

Examples

block_cor = NaN, gene_ensembl = "ensembl", gene_name = "gene_name" ) -#> 2024-10-22 13:34:42.932457 running the baseline pairwise model -#> 2024-10-22 13:34:42.95068 computing pairwise statistics +#> 2024-10-22 13:38:54.176944 running the baseline pairwise model +#> 2024-10-22 13:38:54.194086 computing pairwise statistics head(results_pairwise_nan) #> t_stat_G0-G1 t_stat_G0-G2M t_stat_G0-S t_stat_G1-G2M t_stat_G1-S #> Gene_0001 -0.2419770 0.30095840 0.29195379 0.5429354 0.5339308 diff --git a/reference/registration_wrapper.html b/reference/registration_wrapper.html index 1de13c33..0dcb6305 100644 --- a/reference/registration_wrapper.html +++ b/reference/registration_wrapper.html @@ -22,7 +22,7 @@ spatialLIBD - 1.17.8 + 1.17.9 @@ -200,18 +200,18 @@

Examples

sce, "Cell_Cycle", "sample_id", c("age"), "ensembl", "gene_name", "wrapper" ) -#> 2024-10-22 13:34:43.481554 make pseudobulk object -#> 2024-10-22 13:34:43.638667 dropping 9 pseudo-bulked samples that are below 'min_ncells'. -#> 2024-10-22 13:34:43.660478 drop lowly expressed genes -#> 2024-10-22 13:34:43.71599 normalize expression -#> 2024-10-22 13:34:43.774521 create model matrix -#> 2024-10-22 13:34:43.813457 run duplicateCorrelation() -#> 2024-10-22 13:34:46.26438 The estimated correlation is: -0.0783081238514532 -#> 2024-10-22 13:34:46.267247 computing enrichment statistics -#> 2024-10-22 13:34:46.387901 extract and reformat enrichment results -#> 2024-10-22 13:34:46.414958 running the baseline pairwise model -#> 2024-10-22 13:34:46.434078 computing pairwise statistics -#> 2024-10-22 13:34:46.510731 computing F-statistics +#> 2024-10-22 13:38:54.705986 make pseudobulk object +#> 2024-10-22 13:38:54.855254 dropping 9 pseudo-bulked samples that are below 'min_ncells'. +#> 2024-10-22 13:38:54.876318 drop lowly expressed genes +#> 2024-10-22 13:38:54.929357 normalize expression +#> 2024-10-22 13:38:55.021009 create model matrix +#> 2024-10-22 13:38:55.033263 run duplicateCorrelation() +#> 2024-10-22 13:38:57.365731 The estimated correlation is: -0.0783081238514532 +#> 2024-10-22 13:38:57.368384 computing enrichment statistics +#> 2024-10-22 13:38:57.486334 extract and reformat enrichment results +#> 2024-10-22 13:38:57.512208 running the baseline pairwise model +#> 2024-10-22 13:38:57.530169 computing pairwise statistics +#> 2024-10-22 13:38:57.635923 computing F-statistics diff --git a/reference/run_app.html b/reference/run_app.html index 9aaf209d..fbae3738 100644 --- a/reference/run_app.html +++ b/reference/run_app.html @@ -19,7 +19,7 @@ spatialLIBD - 1.17.8 + 1.17.9 diff --git a/reference/sce_to_spe.html b/reference/sce_to_spe.html index 853eaf47..5d23ea70 100644 --- a/reference/sce_to_spe.html +++ b/reference/sce_to_spe.html @@ -21,7 +21,7 @@ spatialLIBD - 1.17.8 + 1.17.9 @@ -127,7 +127,7 @@

Examples

## Transform it to a SpatialExperiment object spe <- sce_to_spe(sce) } -#> 2024-10-22 13:34:48.685574 loading file /github/home/.cache/R/BiocFileCache/1d0868184ba3_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-10-22 13:39:00.161771 loading file /github/home/.cache/R/BiocFileCache/1d067b86505d_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 diff --git a/reference/sig_genes_extract.html b/reference/sig_genes_extract.html index 4ccd5cb6..0110cb1b 100644 --- a/reference/sig_genes_extract.html +++ b/reference/sig_genes_extract.html @@ -21,7 +21,7 @@ spatialLIBD - 1.17.8 + 1.17.9 @@ -156,9 +156,9 @@

Examples

if (!exists("modeling_results")) { modeling_results <- fetch_data(type = "modeling_results") } -#> 2024-10-22 13:35:01.833116 loading file /github/home/.cache/R/BiocFileCache/123837aa8e57_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1 +#> 2024-10-22 13:39:13.770924 loading file /github/home/.cache/R/BiocFileCache/12397eec449a_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1 if (!exists("sce_layer")) sce_layer <- fetch_data(type = "sce_layer") -#> 2024-10-22 13:35:02.82954 loading file /github/home/.cache/R/BiocFileCache/123855dc376b_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-10-22 13:39:15.066851 loading file /github/home/.cache/R/BiocFileCache/123965771ab_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1 ## anova top 10 genes sig_genes_extract( diff --git a/reference/sig_genes_extract_all.html b/reference/sig_genes_extract_all.html index 99246620..fd6649d4 100644 --- a/reference/sig_genes_extract_all.html +++ b/reference/sig_genes_extract_all.html @@ -19,7 +19,7 @@ spatialLIBD - 1.17.8 + 1.17.9 @@ -128,9 +128,9 @@

Examples

if (!exists("modeling_results")) { modeling_results <- fetch_data(type = "modeling_results") } -#> 2024-10-22 13:35:05.398997 loading file /github/home/.cache/R/BiocFileCache/123837aa8e57_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1 +#> 2024-10-22 13:39:17.671422 loading file /github/home/.cache/R/BiocFileCache/12397eec449a_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1 if (!exists("sce_layer")) sce_layer <- fetch_data(type = "sce_layer") -#> 2024-10-22 13:35:06.374513 loading file /github/home/.cache/R/BiocFileCache/123855dc376b_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-10-22 13:39:19.021849 loading file /github/home/.cache/R/BiocFileCache/123965771ab_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1 ## top 10 genes for all models sig_genes_extract_all( diff --git a/reference/sort_clusters.html b/reference/sort_clusters.html index b5eb5ff8..90509959 100644 --- a/reference/sort_clusters.html +++ b/reference/sort_clusters.html @@ -19,7 +19,7 @@ spatialLIBD - 1.17.8 + 1.17.9 diff --git a/reference/spatialLIBD-package.html b/reference/spatialLIBD-package.html index 2fd35636..a58367b3 100644 --- a/reference/spatialLIBD-package.html +++ b/reference/spatialLIBD-package.html @@ -18,7 +18,7 @@ spatialLIBD - 1.17.8 + 1.17.9 diff --git a/reference/tstats_Human_DLPFC_snRNAseq_Nguyen_topLayer.html b/reference/tstats_Human_DLPFC_snRNAseq_Nguyen_topLayer.html index 0d22375b..00b0f387 100644 --- a/reference/tstats_Human_DLPFC_snRNAseq_Nguyen_topLayer.html +++ b/reference/tstats_Human_DLPFC_snRNAseq_Nguyen_topLayer.html @@ -23,7 +23,7 @@ spatialLIBD - 1.17.8 + 1.17.9 diff --git a/reference/vis_clus.html b/reference/vis_clus.html index 69fdd452..04fdf39f 100644 --- a/reference/vis_clus.html +++ b/reference/vis_clus.html @@ -19,7 +19,7 @@ spatialLIBD - 1.17.8 + 1.17.9 @@ -242,7 +242,7 @@

Examples

) print(p4) } -#> 2024-10-22 13:35:08.945058 loading file /github/home/.cache/R/BiocFileCache/1d0868184ba3_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-10-22 13:39:22.136622 loading file /github/home/.cache/R/BiocFileCache/1d067b86505d_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 diff --git a/reference/vis_clus_p.html b/reference/vis_clus_p.html index 7f15da7a..bb20b44a 100644 --- a/reference/vis_clus_p.html +++ b/reference/vis_clus_p.html @@ -20,7 +20,7 @@ spatialLIBD - 1.17.8 + 1.17.9 @@ -202,7 +202,7 @@

Examples

## Clean up rm(spe_sub) } -#> 2024-10-22 13:35:28.401729 loading file /github/home/.cache/R/BiocFileCache/1d0868184ba3_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-10-22 13:39:42.240837 loading file /github/home/.cache/R/BiocFileCache/1d067b86505d_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 diff --git a/reference/vis_gene.html b/reference/vis_gene.html index a148dd74..8d67292e 100644 --- a/reference/vis_gene.html +++ b/reference/vis_gene.html @@ -20,7 +20,7 @@ spatialLIBD - 1.17.8 + 1.17.9 @@ -341,7 +341,7 @@

Examples

) print(p8) } -#> 2024-10-22 13:35:43.384444 loading file /github/home/.cache/R/BiocFileCache/1d0868184ba3_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-10-22 13:39:57.748229 loading file /github/home/.cache/R/BiocFileCache/1d067b86505d_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 diff --git a/reference/vis_gene_p.html b/reference/vis_gene_p.html index 9e213dd7..96a0f138 100644 --- a/reference/vis_gene_p.html +++ b/reference/vis_gene_p.html @@ -21,7 +21,7 @@ spatialLIBD - 1.17.8 + 1.17.9 @@ -215,7 +215,7 @@

Examples

## Clean up rm(spe_sub) } -#> 2024-10-22 13:36:09.302824 loading file /github/home/.cache/R/BiocFileCache/1d0868184ba3_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-10-22 13:40:23.670459 loading file /github/home/.cache/R/BiocFileCache/1d067b86505d_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 diff --git a/reference/vis_grid_clus.html b/reference/vis_grid_clus.html index 46b2444e..c7666982 100644 --- a/reference/vis_grid_clus.html +++ b/reference/vis_grid_clus.html @@ -19,7 +19,7 @@ spatialLIBD - 1.17.8 + 1.17.9 @@ -237,7 +237,7 @@

Examples

## for subject 3 cowplot::plot_grid(plotlist = p_list, ncol = 2) } -#> 2024-10-22 13:36:24.40968 loading file /github/home/.cache/R/BiocFileCache/1d0868184ba3_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-10-22 13:40:39.220053 loading file /github/home/.cache/R/BiocFileCache/1d067b86505d_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 diff --git a/reference/vis_grid_gene.html b/reference/vis_grid_gene.html index 18eecb8d..d162de0b 100644 --- a/reference/vis_grid_gene.html +++ b/reference/vis_grid_gene.html @@ -20,7 +20,7 @@ spatialLIBD - 1.17.8 + 1.17.9 @@ -256,7 +256,7 @@

Examples

## for subject 3 cowplot::plot_grid(plotlist = p_list, ncol = 2) } -#> 2024-10-22 13:36:41.009364 loading file /github/home/.cache/R/BiocFileCache/1d0868184ba3_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-10-22 13:40:55.851199 loading file /github/home/.cache/R/BiocFileCache/1d067b86505d_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1